mlink-pedin
ilink-pedin
linkmap-pedin
To get better protection against a crash, we can use an auxiliary program ckpt, but this is not for novices. See: FD: README.checkpoint.
Here is what the 3 final.out files will look like. First, mlink-final.out:
MLINK
Pedigree File : pedin.tpd
Parameter File : datain.tdt
Output Pedigree File : pedfile.dat
Output Parameter File : datafile.dat
Log File : lsp.log
Stream File : lsp.stm
Date Run : 7-Nov-95 12:51:21
Sex Difference : 0
Recomb. Fraction to Vary : 1
Increment Value : 2.00000000
Stop Value : 1.00000000
Locus Order : 1 2
Male Recomb. Fractions : 0.00000000
Initial Recomb. Fraction : 0.01000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.05000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.10000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.20000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.30000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.40000000
Increment Value : 2.00000000
Stop Value : 1.00000000
LINKAGE (V5.1) WITH 2-POINT AUTOSOMAL DATA
ORDER OF LOCI: 1 2
THETAS 0.500
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -19.273056 -8.370164
-----------------------------------
TOTALS -19.273056 -8.370164
-2 LN(LIKE) = 3.85461e+01 LOD SCORE = 0.000000
THETAS 0.000
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -100000000000000000000.000000 -43429355638650388480.000000
-----------------------------------
TOTALS -100000000000000000000.000000 -43429355638650388480.000000
-2 LN(LIKE) = 2.00000e+20 LOD SCORE = -43429355638650388480.000000
THETAS 0.010
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -21.145838 -9.183501
-----------------------------------
TOTALS -21.145838 -9.183501
-2 LN(LIKE) = 4.22917e+01 LOD SCORE = -0.813337
THETAS 0.050
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -19.701227 -8.556116
-----------------------------------
TOTALS -19.701227 -8.556116
-2 LN(LIKE) = 3.94025e+01 LOD SCORE = -0.185952
THETAS 0.100
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -19.223124 -8.348479
-----------------------------------
TOTALS -19.223124 -8.348479
-2 LN(LIKE) = 3.84462e+01 LOD SCORE = 0.021685
THETAS 0.200
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -18.986975 -8.245921
-----------------------------------
TOTALS -18.986975 -8.245921
-2 LN(LIKE) = 3.79740e+01 LOD SCORE = 0.124243
THETAS 0.300
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -19.055367 -8.275623
-----------------------------------
TOTALS -19.055367 -8.275623
-2 LN(LIKE) = 3.81107e+01 LOD SCORE = 0.094541
THETAS 0.400
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -19.200549 -8.338675
-----------------------------------
TOTALS -19.200549 -8.338675
-2 LN(LIKE) = 3.84011e+01 LOD SCORE = 0.031489
MLINK
Pedigree File : pedin.tpd
Parameter File : datain.tdt
Output Pedigree File : pedfile.dat
Output Parameter File : datafile.dat
Log File : lsp.log
Stream File : lsp.stm
Date Run : 7-Nov-95 12:51:24
Sex Difference : 0
Recomb. Fraction to Vary : 1
Increment Value : 2.00000000
Stop Value : 1.00000000
Locus Order : 1 3
Male Recomb. Fractions : 0.00000000
Initial Recomb. Fraction : 0.01000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.05000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.10000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.20000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.30000000
Increment Value : 2.00000000
Stop Value : 1.00000000
Initial Recomb. Fraction : 0.40000000
Increment Value : 2.00000000
Stop Value : 1.00000000
LINKAGE (V5.1) WITH 2-POINT AUTOSOMAL DATA
ORDER OF LOCI: 1 2
THETAS 0.500
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -12.459367 -5.411023
-----------------------------------
TOTALS -12.459367 -5.411023
-2 LN(LIKE) = 2.49187e+01 LOD SCORE = 0.000000
THETAS 0.000
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -100000000000000000000.000000 -43429355638650388480.000000
-----------------------------------
TOTALS -100000000000000000000.000000 -43429355638650388480.000000
-2 LN(LIKE) = 2.00000e+20 LOD SCORE = -43429355638650388480.000000
THETAS 0.010
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -14.332149 -6.224360
-----------------------------------
TOTALS -14.332149 -6.224360
-2 LN(LIKE) = 2.86643e+01 LOD SCORE = -0.813337
THETAS 0.050
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -12.887538 -5.596975
-----------------------------------
TOTALS -12.887538 -5.596975
-2 LN(LIKE) = 2.57751e+01 LOD SCORE = -0.185952
THETAS 0.100
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -12.409435 -5.389338
-----------------------------------
TOTALS -12.409435 -5.389338
-2 LN(LIKE) = 2.48189e+01 LOD SCORE = 0.021685
THETAS 0.200
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -12.173286 -5.286780
-----------------------------------
TOTALS -12.173286 -5.286780
-2 LN(LIKE) = 2.43466e+01 LOD SCORE = 0.124243
THETAS 0.300
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -12.241679 -5.316482
-----------------------------------
TOTALS -12.241679 -5.316482
-2 LN(LIKE) = 2.44834e+01 LOD SCORE = 0.094541
THETAS 0.400
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
1 -12.386861 -5.379534
-----------------------------------
TOTALS -12.386861 -5.379534
-2 LN(LIKE) = 2.47737e+01 LOD SCORE = 0.031489
Notice that the Lod score for each candidate theta is shown. The Lodscore is the difference between the entry in the LOG 10 LIKE column for that theta and theta = 0.5. The large numbers are -infinity, indicating that theta cannot be 0, because there is an obligatory recombinant.
Now, let us see ilink-final.out:
ILINK
Pedigree File : pedin.tpd
Parameter File : datain.tdt
Output Pedigree File : pedfile.dat
Output Parameter File : datafile.dat
Log File : lsp.log
Stream File : lsp.stm
Date Run : 7-Nov-95 12:51:32
Sex Difference : 0
Interference : 0
Locus Order : 2 3
Male Recomb. Fractions : 0.10000000
CHROMOSOME ORDER OF LOCI :
1 2
THETAS:
0.500
-2 LN(LIKE) = 3.38332e+01
LOD SCORE =-6.76864e-09
NUMBER OF ITERATIONS = 4
NUMBER OF FUNCTION EVALUATIONS = 11
PTG = -5.44302e-07
ILINK shows that the best estimate of theta between markers 2 and 3 is 0.5, so they are probably not on the same chromosome arm.
Finally, let us look at linkmap-final.out:
LINKMAP
Pedigree File : pedin.tpd
Parameter File : datain.tdt
Output Pedigree File : pedfile.dat
Output Parameter File : datafile.dat
Log File : lsp.log
Stream File : lsp.stm
Date Run : 7-Nov-95 12:51:41
Sex Difference : 0
Test Locus : 1
Stop Value : 0.00000000
Number of Evaluations : 5
Locus Order : 1 2 3
Male Recomb. Fractions : 0.50000000 0.25000000
THETAS 0.500 0.250
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.899877 -10.813856
-2 LN(LIKE) = 4.97998e+01
THETAS 0.400 0.250
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.827371 -10.782367
-2 LN(LIKE) = 4.96547e+01
THETAS 0.300 0.250
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.682189 -10.719316
-2 LN(LIKE) = 4.93644e+01
THETAS 0.200 0.250
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.613797 -10.689613
-2 LN(LIKE) = 4.92276e+01
THETAS 0.100 0.250
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.849945 -10.792171
-2 LN(LIKE) = 4.96999e+01
THETAS 0.000 0.250
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -100000000000000000000.000000 -43429355638650388480.000000
-2 LN(LIKE) = 2.00000e+20
LINKMAP
Pedigree File : =
Parameter File : datain.tdt
Output Pedigree File : pedfile.dat
Output Parameter File : datafile.dat
Log File : lsp.log
Stream File : lsp.stm
Date Run : 7-Nov-95 12:51:45
Sex Difference : 0
Test Locus : 1
Stop Value : 0.25000000
Number of Evaluations : 5
Locus Order : 2 1 3
Male Recomb. Fractions : 0.00000000 0.25000000
THETAS 0.000 0.250
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -100000000000000000000.000000 -43429355638650388480.000000
-2 LN(LIKE) = 2.00000e+20
THETAS 0.050 0.222
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.466375 -10.625589
-2 LN(LIKE) = 4.89327e+01
THETAS 0.100 0.187
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -23.994311 -10.420575
-2 LN(LIKE) = 4.79886e+01
THETAS 0.150 0.143
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -23.878945 -10.370472
-2 LN(LIKE) = 4.77579e+01
THETAS 0.200 0.083
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.098045 -10.465626
-2 LN(LIKE) = 4.81961e+01
THETAS 0.250 0.000
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -100000000000000000000.000000 -43429355638650388480.000000
-2 LN(LIKE) = 2.00000e+20
LINKMAP
Pedigree File : =
Parameter File : datain.tdt
Output Pedigree File : pedfile.dat
Output Parameter File : datafile.dat
Log File : lsp.log
Stream File : lsp.stm
Date Run : 7-Nov-95 12:51:48
Sex Difference : 0
Test Locus : 1
Stop Value : 0.50000000
Number of Evaluations : 5
Locus Order : 2 3 1
Male Recomb. Fractions : 0.25000000 0.00000000
THETAS 0.250 0.000
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -100000000000000000000.000000 -43429355638650388480.000000
-2 LN(LIKE) = 2.00000e+20
THETAS 0.250 0.100
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.849945 -10.792171
-2 LN(LIKE) = 4.96999e+01
THETAS 0.250 0.200
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.613797 -10.689613
-2 LN(LIKE) = 4.92276e+01
THETAS 0.250 0.300
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.682189 -10.719316
-2 LN(LIKE) = 4.93644e+01
THETAS 0.250 0.400
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.827371 -10.782367
-2 LN(LIKE) = 4.96547e+01
THETAS 0.250 0.500
-----------------------------------
PEDIGREE | LN LIKE | LOG 10 LIKE
-----------------------------------
TOTALS -24.899877 -10.813856
-2 LN(LIKE) = 4.97998e+01
To get lod scores compare the LOG 10 LIKE column entry for your candidate theta against the entry for theta = 0.5 (which means 1 is unlinked to both 2 and 3). This is the first and last entry in the output table.